I would prefer using the side view orientation. However, after I flip pages the last couple of lines from the previous page are repeated at the beginning of the next page. This is very very annoying. Does this happen to everyone or do I have a lemon? Or am I the only one who prefers this orientation?

It shows the last couple of lines so you know that you do not miss anything. It's there to keep the placement. It may also, on pdf files (maybe others, show the bottom of the first half a lighter shade and the top of the second half to show that is where the page was broken. It is normal.

It's because the landscape view shows single pages in two halves - first the top half and then the second half. You see slightly more than half a page in each view, however, so there is an overlap region. If you look closely, you'll see that this region is shaded differently to the rest of the page.